This study investigates stagnant atmospheric conditions in Almaty, Kazakhstan, a city nestled within a complex terrain. These conditions, characterized by weak local winds and inversion layers, trap pollutants within the city, particularly during winter. The Weather Research & Forecasting (WRF) model was employed to simulate atmospheric conditions using Local Climate Zone data. Verification of the model’s accuracy was achieved through comparisons with data from weather stations and the Landsat-9 satellite. The model successfully reproduced the observed daily temperature variations and weak winds during the testing period (13–23 January 2023). Comparisons with radiosonde data revealed good agreement for morning temperature profiles, while underestimating the complexity of the evening atmospheric structure. The analysis focused on key air quality factors, revealing cyclical patterns of ground-level and elevated inversions linked to mountain-valley circulation. The model effectively captured anabatic and katabatic flows. The study further examined the urban heat island (UHI) using a virtual rural method. The UHI exhibited daily variations in size and temperature, with heat transported by prevailing winds and katabatic flows. Statistical analysis of temperature and wind patterns under unfavorable synoptic situations revealed poor ventilation in Almaty. Data from three Januaries (2022/2023/2024) were used to create maps showing average daytime and nighttime air temperatures, wind speed, and frequency of calm winds.